BIRC6 RNAseq
## [1] "Max fold diff lib size = 1.75956241223834"
## [1] "57820 total transcripts. Keeping 17782 transcripts after filtering"QC checks
Heirarchical clustering
Heirarchical clustering based on expression profile Spearman correlations. This shows that the data are overall high quality (no outliers), with good grouping of samples within-cell lines. The biggest difference is clearly between colon and ovarian cell lines.
Multi-dimensional scaling
PCA
lCPM distributions
Comparing distribution of log-counts per million per sample looks reasonable
Replicate correlations
Comparing BIRC6 expression levels
## `summarise()` has grouped output by 'samp_pert', 'cell_line'. You can override
## using the `.groups` argument.## # A tibble: 6 × 4
## # Groups: samp_pert, cell_line [6]
## samp_pert cell_line perturbation BIRC6_GE
## <chr> <chr> <chr> <dbl>
## 1 HCC15.sgBIRC6.1 HCC15 sgBIRC6.1 5.68
## 2 HCC15.sgBIRC6.4 HCC15 sgBIRC6.4 5.61
## 3 HCC15.sgCh2.2 HCC15 sgCh2.2 6.66
## 4 HCC202.sgBIRC6.1 HCC202 sgBIRC6.1 6.16
## 5 HCC202.sgBIRC6.4 HCC202 sgBIRC6.4 5.78
## 6 HCC202.sgCh2.2 HCC202 sgCh2.2 7.00
Collapse replicates
Save LCPM data (rep collapsed)
Diff expression analysis
Collapse across replicates by summing read counts Model cell line as random effect
DE in BIRC6 Dependent lines
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## Attaching package: 'scales'## The following object is masked from 'package:readr':
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GSEA
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
DE in BIRC6 Independent lines
GSEA
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
Comparison of DE in Dependent vs Independent lines
Estimated KO effect in Dependent - Independent lines
GSEA
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
Average DE across all cell lines
GSEA
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
#model individual cell line effects
GSEA
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"## Rows: 50 Columns: 8
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## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
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## Rows: 50 Columns: 8
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## chr (2): pathway, leadingEdge
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## Rows: 50 Columns: 8
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## chr (2): pathway, leadingEdge
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## ℹ Use `spec()` to retrieve the full column specification for this data.
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## Rows: 50 Columns: 8
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## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
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## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
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## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
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## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.